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CURRICULUM VITAE EUROPEAN FORMAT PERSONAL INFORMATION Name, Surname Address House number, street name, postcode, city, country Telephone Fax E-mail O. Ugur Sezerman Sabanci University MDBF 34056 Orhanli Tuzla ISTANBUL TURKEY +90-542 422 36 88 +90 216 483 95 50 [email protected] Website Nationality Place and Date of birth Turkish IZMIR TURKEY 25 June 1964 WORK EXPERIENCE 9/99Faculty. Biological Sciences and Bioengineering Dept.,Sabanci University, Istanbul,TURKEY 8/98-9/99 Part-Time Faculty, Computer Engineering Dept., Bogazici University,Istanbul, TURKEY 1/93-5/97 Post-Doc , Biomedical Engineering, Boston University 2/90-1/93 Research Assistant, Biomedical Engineering, Boston University 9/87-5/89 Teaching Assistant, Biomedical Engineering, Boston University 1/85-1/87 Research Assistant, Biomedical Engineering, Bogazici University 1/83-1/85 Teaching Assistant, Mathematics Dept., Bogazici University,Istanbul Name and address of employer Type of business or sector Occupation or position held Main activities and responsibilities Page 1 - Curriculum vitae of Sezerman Sabanci University Engineering and Natural Sciences Faculty 34956 Orhanli Tuzla ISTANBUL Academia Associate Professor Head of the Computational Biology Lab, Head of the Protein Engineering Lab EDUCATION AND TRAINING 9/87-1/93 Dates (from – to) Ph.D. Biomedical Engineering, Boston University, Boston, MA, USA. Thesis: New Methods for Molecular Docking with Applications to Recognition and Design Problems in Immunology with Prof. Charles DeLisi 9/85-8/87 M.S. Biomedical Engineering, Bogazici University, Istanbul, TURKEY 1/85-12/87 Name and type of organisation providing education and training Principal subjects occupational skills covered Title of qualification awarded Level in National classification B.S. Electrical Engineering, Bogazici University, Istanbul,TURKEY Boston University, Boston USA Programming, Molecular Modeling, Bioinformatics, Protein engineering Ph. D. In Biomedical Engineering Associate professor RESEARCH ACTIVITIES Research sectors Recent Scientific Activities. Page 2 - Curriculum vitae of Sezerman Bioinformatics, Protein Engineering Established Computational Biology Lab at Sabanci University Established Protein Engineering Lab at Sabanci University Established Fermentation Lab at Sabanci University Organized Protein Engineering Workshop, Structural Biology Workshop, Non Coding RNA Workshop funded by European Science Foundation in Turkey Books and Articles C. DeLisi, U. Sezerman and R. Rosenfeld,”Problems and Progress on Computational Approaches to the Molecular Basis of Cell Recognition.” 25th Jerusalem Symposium on Biochemistry and Quantum Chemistry, Pullman and Jortner eds. Kluwer Academic Publishers, Amsterdam S. Vajda, M.S. Jafri, O.U. Sezerman, “Necessary Conditions for Avoiding Incorrect Polypeptide Folds in Conformational Search by Energy Minimization”, Biopolymers, 33, 173-192 (1993). U. Sezerman, S. Vajda, J. Cornette, C. DeLisi, “ Towards Computational Determination of Peptide-Receptor Structure”, Protein Science, 2, 1827-1843 (1993) G. Vasmatzis, J. Cornette, U. Sezerman, C. DeLisi, “TCR Recognition of the MHC-Peptide Dimer: Structural Properties of a Ternary Complex”, J. Mol. Biol. 261, 72-89 (1996). U. Sezerman, S. Vajda, C. Delisi, “Free Energy Mapping of Class I MHC molecules and Structural Determination of Bound Peptides”, Protein Science 5, 1272-1281(1996). Z. Isik, B. Yanikoglu, U. Sezerman “Protein Structural Class Determination Using Support Vector Machines”, Lecture Notes in Computer Science, Oct. 2004. Bilecen, K., Ozturk, U.H., Duru, A.D., Sutlu, T., Petoukhov, M.V., Svergun, D.I., Koch, M.H.J., Sezerman, U.O., Cakmak, I., and Sayers, Z.” Triticum durum metallothionein: isolation of the gene and structural characterization of the protein using solution scattering and molecular modeling.” J. Biol. Chem. 280:13701-113711 (2005). Bakir B., Sezerman U. “Functional Classification of G-Protein Coupled Receptors, Based on Their Specific Ligand Coupling Patterns” Lecture Notes in Computer Science (LNCS), Vol. 3907, April 2006. Yardimci G.G., Kucukural A., Saygin Y, and Sezerman U.,”Modified Association Rule Mining Approach for the MHC-Peptide Binding Problem”, LNCS volume 4263,(2006). Erguner B., Erdogan O., and Sezerman U.,”Prediction and Classification for GPCR Sequences Based on Ligand Specific Features”, LNCS volume 4263,( 2006). Budak H., Kasap Z., Shearman R. C., Dweikat I.,Sezerman U. and Mahmood A. “Molecular Characterization of cDNA encoding resistance gene-like sequences in Buclo dactiloides”, Molecular Biotechnology. 34:293-301 ( 2006). Gul O., Calay E., Sezerman U., Basaga H., Gurbuz Y.,”Sandwich type antibody microarryas for the detection and quantification of cardiovascular risk markers”, Sensors and Actuators, 125, 581-588 (2007). Erdoğmuş M., Sezerman U., “Application of automatic mutation gene pair extraction to diseases”,Journal of Bioinformatics and Computational Biology, Vol.5, Issue 6,:1261-1275 (2007). Meydan C., Yörükoğlu D., Küçükural A., Sezerman U., “Discovery of biomarkers for hexachlorobenzene toxicity using population based methods on gene expression data”, Lecture Notes in Computer Science, Vol.5265,412-423, 2008. Kallempudi S., Gül Ö., Başağa H., Sezerman U., Gurbuz Y.,“Label-free biosensors for the detection and quantification of cardiovascular risk markers”, Journal of Sensor Letters, Vol.6, Cakici S., Sumengen S., Sezerman U., Balcısoy S., “DockPro: A VR-Based Tool for ProteinProtein Docking Problem”, International Journal of Virtual Reality, 2008. Yeniterzi S., Sezerman U. “EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts” BMC Bioinformatics. 10(Suppl 8): S2, 2009. Solda G., Makunin I., Sezerman U., Corti G., Guffanti A., “An Ariadne's thread to the Page 3 - Curriculum vitae of Sezerman identification and annotation of noncoding RNAs in eukaryotes” , Briefings in Bioinformatics 10(5):475-489 ,2009. Albayrak A, Otu, H. H, Sezerman U.,” Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets”, BMC Bioinformatics, 11:428, 2010. Cobanoglu M.C., Saygin Y., Sezerman U.,“Classification of GPCRs Using Family Specific Motifs”, IEEE Transactions on Comp. Biology and Bioinformatics , ISSN: 1545-5963, 2010. Meydan, C. and Sezerman, U., "Biomarker discovery for toxicity", Neurocomputing (Sp. Iss. SI), Vol.73, No.13-15, 2384-2393, 2010. Ozgenturk N.O., Oruç F.,Sezerman U., Kucukural A., Korkut S. V., Toksoz F, and Un C., “Generation and Analysis of Expressed Sequence Tags from Olea europaea L.," Comparative and Functional Genomics, vol. 2010, Article ID 757512, doi:10.1155/2010/757512, 2010. Kucukural A, Szilagyi A, Sezerman O, Zhang Y (2010): Protein homology analysis for function prediction with parallel sub-graph isomorphism. In: Lodhi H, Yamanishi Y (eds.): Chemoinformatics and advanced machine learning perspectives: complex computational methods and collaborative perspectives. IGI Global, 2010, pp. 129-144. Book Chapter Akcapinar G.B., Gul O., Sezerman U.,” Effect of codon optimization on the expression of Trichoderma reesei endoglucanase 1 in Pichia pastoris”, Biotechnology Progress, DOI: 10.1002/btpr.663, 2011. Seidl-Seiboth V, Guber S, Sezerman U, Schwecke T, Albayrak A, Neuhof T, Döhren H, Baker SE and Kubicek CP. Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation, and processing J. Mol. Evol. Volume 72, Number 4, 339-351, 2011. Albayrak A., Sezerman U., “Discrimination of thermophilic and mesophilic proteins using reduced amino acid alphabets with n-grams” in Press Current Bioinformatics, 2011. Akcapinar G.B., Sezerman U.,” From in silico to in vitro: Modelling and production of Trichoderma reesei endoglucanase 1 and its mutant in Pichia pastoris” Accepted with minor revisions. J. Biotechnology Page 4 - Curriculum vitae of Sezerman ULTERIORI INFORMAZIONI / ADDITIONAL INFORMATION Refereed Conference Publications Meydan, Cem and Sezerman, Uğur and Otu, Hasan, "Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining", Zhang, J. and Li, G. Z. and Yang, J. Y. (eds.), International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009 (IJCBS '09), USA: IEEE (Institute of Electrical and Electronics Engineers), August 2009, 315-318 Bakış, Yasin and Sezerman, Uğur and Babaç, M. Tekin and Meydan, Cem, "Optimization of morphological data in numerical taxonomy analysis using genetic algorithms feature selection method", 11th Genetic and Evolutionary Computation Conference, GECCO 2009, New York, NY, USA: ACM (Association for Computing Machinery), July 2009, 1967-1970 Yörükoğlu, Deniz and Bakış, Yasin and Sezerman, Uğur, "An entropy based heuristic model for predicting functional sub-type divisions of protein families", 11th Genetic and Evolutionary Computation Conference, GECCO 2009, New York, NY, USA: ACM (Association for Computing Machinery), July 2009, 2173-2178 Meydan, Cem and Otu, Hasan and Sezerman, Uğur, "Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining", 4th International Symposium on Health Informatics and Bioinformatics (HIBIT 09), Ankara: ODTU (Ortadoğu Teknik Üniversitesi), April 2009 Cem Meydan, Alper Kucukural, Uğur Sezerman,”Biomarker detection for hexachlorobenzene toxicity using genetic algorithms on gene expression data” HIBIT08, Istanbul, 2008. Burak Aksu, Nihan Özsamli, Kemal Kılıç, Uğur Sezerman,”A Modified framework for feature subset selection in microarray data” HIBIT08 , Istanbul, 2008. Süveyda Yeniterzi, Reyyan Yeniterzi, Alper Küçükural, Nilay Noyan, Uğur Sezerman “A new approach to measure the similarities of protein structures using network properties”, HIBIT08, İstanbul,2008. Alper Küçükural, Uğur Sezerman, Aytül Erçil, ”Discrimination of Native Folds Using Network Properties of Protein Structures”, APBC 2008,Kyoto,2008. Alper Küçükural, Reyyan Yeniterzi, Süveyda Yeniterzi, Uğur Sezerman, ”Evolutionary selection of minimum number of features for classification of gene expression data using genetic algorithms” ,ACM Genetic And Evolutionary Computation Conference (GECCO 2007),London, 2007. Alper Küçükural, Uğur Sezerman, ”Potential use of graph theoretical properties of protein structures in structural alignment”, BIOCOMP 2007, Las Vegas,2007. Alper Küçükural, Uğur Sezerman, “Detecting Native Proteins in ROSETTA Dataset Using Graph Properties” ,HIBIT2007, Antalya,2007. Reyyan Yeniterzi, Süveyda Yeniterzi, Alper Küçükural, Uğur Sezerman, ”Feature selection with genetic algorithms on cardiac arrhytmia database”, HIBIT ,Antalya,2007. Ugur Sezerman, A.Akalin, Z.Kasap, E.Kavak, “Ligand-specific classification of G protein-coupled receptors using support vector machines and reduced alphabeth”, FEBS Journal 2006 273:p1 42, Istanbul,2006. Özgür Gül, Ercihan İncetürkmen, Hüveyda Başağa, Uğur Sezerman, Yaşar Gurbuz, ”Biosensor implementation for cardiovascular risk marker analysis” IEEE Sensors 2005 Conference, Korea,2005. A.Akalın, Z.Kasap, E. Kavak, U.Sezerman “Classification of GPCRs according to their ligand specifity using SVMs”, BIYOMUT Conference , May-27-30, 2004.Istanbul Turkey. Y. Turkeli, A Ercil, U. Sezerman “Effect of Feature Extraction and Feature Selection on Expression Data from Epithelial Ovarian Cancer” IEEE EMBC 2003. Y. Turkeli, U. Sezerman, F. Gurgen, “Information excavation from Scale free genetic networks using attributed graph matching”, ICANN 2003. A. Akyol, U. Sezerman, “Fold Classification of Protein Sequences by GeneticAlgorithm”, ICANN 2003. U. Sezerman, R. Islamaj, E. Alpaydin,” Three dimensional representation of Amino Acids using Machine Learning methods” IEEE EMBC (2001). Page 5 - Curriculum vitae of Sezerman